Focusing mechanisms for microscopes are employed to position the object at the plane of focus of the instrument, to enable the object to be examined, i.e. inspected, illuminated or otherwise acted upon. Typically the object is placed upon a platform that moves laterally relative to the optical axis of the objective, to bring the area of interest of the object into alignment with the optical axis. The platform is then raised or lowered (translated) along the optical axis to achieve best focus. If it is necessary to register the optical axis with regions of the object larger than the field of view of the objective lens, the platform and object are further moved laterally in a sequence of steps to view the entire area. In some cases, microscopes are constructed to translate the objective lens or the entire microscope along the optical axis to reach best focus and in some cases the objective lens is moved laterally to bring the optical axis and areas of interest into alignment.
A known technique for translating the platform and object in the direction of the optical axis employs a precision dovetail mechanism that is activated by a manual rack and pinion or a motorized lead screw. In many cases this mechanism must be constructed with high accuracy to be capable of micron or sub-micron positional resolution, which results in high cost.
In the case of wide field of view microscopes in which lateral motion of the object or microscope objective is required, such as flying objective scanners, there is need for reliable, low cost and fast focus mechanisms of high accuracy. This need exists particularly in respect of investigational tools for biology, e.g., for viewing arrays of fluorescently labeled microorganisms and DNA assays as well as for viewing entire biopsy samples, which may be as large as a square centimeter or larger. (xe2x80x9cDNAxe2x80x9d is used here to designate the full range of nucleic acids of interest to the field of biotechnology.) In particular low cost reading of biochips such as the xe2x80x9cGene Chip(copyright)xe2x80x9d by Affymetrix Inc., and of high density spotted micro arrays or microscope slides is a widely felt need.
According to present biological analytical technology, arrays of fluorescently labeled microorganisms and DNA assays are created in two dimensional fields. The objects to be examined in an array are, for example, DNA fragments that have discriminating sequence information. Biological laboratories have targeted round or square objects for the arrays (e.g., spots of DNA) of diameters or side dimensions of the order of 20 to 250 micron, the spot size depending primarily upon the total number of objects to be represented in the array.
DNA arrays are typically probed with fluorescently labeled fragments of potentially complementary strands. When a match occurs between a fragment in a deposited spot and a fluorescently labeled fragment probe, hybridization occurs, and a positive xe2x80x9cscorexe2x80x9d can be recorded under fluoroscopic examination. Because fluorescence, whether natural or stimulated by illumination, is a weak signal, a xe2x80x9cscorexe2x80x9d is identified for a DNA spot by the intensity of the fluorescence from the spot compared to reading(s) for the background that directly surrounds the specific spot. By controlled deposition of spots of a variety of DNA fragments in the array and by observing the matches or xe2x80x9cscoresxe2x80x9d that occur at known spot addresses, important information concerning nucleic acids can be inferred. For this technology to expand widely, economical instruments are required that can rapidly and accurately scan the fluorescently labeled objects over a wide field of view, e.g. a field of view that is approximately 22 mm wide, the useful width of conventional glass microscope slides.
The large volume of data to be evaluated also calls for unattended operation of such instruments upon a sequence of slides or biochips, including automatic focusing of the microscope for each slide, biochip, or other object and in some cases, automatic focusing as scanning of a particular object proceeds.
Microscopes or microscope-like instruments have been developed to inspect, illuminate or otherwise treat wide areas, based on scanning principles. In the case of inspection, the image is constructed electronically from a succession of acquired single picture elements during relative scanning movement between the object and the microscope. Focusing in these instruments is commonly automated, but there are significant economic and operational drawbacks in the systems that have been commercially available.
For a number of reasons, proper focusing is a critical need for automated microscopes where the material to be investigated is disposed over a wide area of a microscope slide or located on a window of a biochip holder. A microscope slide is typically a slab of float glass approximately 25xc3x9775 mm in x, y dimensions and about 1+0.1/xe2x88x920.2 mm thick as defined by industrial standard ISO 8037-1-1986E. It is common for microscope slides to be slightly bowed, as they are not very rigid and can be deformed when clamped. In the normal installation of a slide in a microscope, the slide is caused to rest upon a flat surface and is held in place by gently pushing its edges against stops, a technique which alleviates most deformation. Other types of substrates for microscopic examination, including arrays provided on relatively thin glass cover slips and on plastic substrates or holders, likewise have variation in thickness or shape and are subject to deformation or the area to be viewed does not have an accurate or reliable reference location.
The depth of field (focus tolerance) and the resolution of a given microscope are inter-related, being defined by the laws of physics. The better the resolution, the smaller is the depth of focus. Present day biochip examination calls for pixel resolution between 2 and 10 micron which corresponds to a depth of field between approximately 4 and 200 micron, the particular values depending upon the optical configuration and the application. For pathology, the pixel may have 0.5 micron diameter and the depth of field 2 micron. Since the thickness variation of commercial microscope slides is greater than such values, when the slide rests upon its back surface, repeated focusing of the microscope is compulsory and autofocusing is generally desirable.
In cases where slides or other objects are sufficiently uniform for the purpose at hand, focus is obtained once per slide or object to be microscopically examined, during a setup procedure.
In some cases, automated microscopes employ dynamic focusing features, i.e. features enabling continual adjustment of focus as scanning of a given slide or object proceeds. For this purpose an algorithm is employed to define focus. Commonly, dynamic systems analyze the image acquired through the optical path of the instrument. In response to these readings, the algorithm is employed under computer control, to cause an element of the system to be raised and lowered as scanning proceeds, to translate the object along the optical axis to achieve focus in a dynamic manner. Frequently the pattern of raising and lowering is based upon a prescan of the overall object, from which positional information has been stored for use to control focus during the following examination scan. Typically instruments that enable dynamic focus adjustment with great precision require great cost.
A common attempt to avoid the cost and delays of prior art auto-focus techniques has been to incorporate a mechanism that forces a microscope slide against three buttresses, in an attempt to achieve precise location of the slide. Unfortunately, such techniques have unsatisfactory aspects, in causing the slide to deform, especially with bowing. This frequently results in loss of resolution. Also, such technique can only be used when the surface to be inspected is rigid and co-planar with the buttress reference location.
The present invention provides a novel method and system for focusing a microscope. Though, at its broadest level of generality, it is applicable to all microscopes, it has particular advantage when associated in a system for automatic focusing, and it is presently considered most advantageous when the automatic focusing system is associated with a scanning system in which the object under inspection is translated under either a fixed or moving lens. The invention is especially applicable to instrument systems that operate under computer control such as optical scanners designed for reading biochips constructed on microscope slides or incorporated in a holder such as the Affymetrix xe2x80x9cGene Chip(copyright)xe2x80x9d. While having a special application in achieving low cost automated scanning, in which focus is established once per slide, the invention is also advantageous in performing dynamic focus.
The invention provides a simple and low cost technique to bring the relevant surface (typically the top surface) of a microscope slide or a biochip holder into the focal plane of a microscope by automatic motions of the instrument.
The invention also enables a plurality of objects to be viewed. According to a feature of the invention, each class of object with which the microscope is useful which may have e.g., different thickness or other dimensions, is provided a xe2x80x9cspecial purpose locationxe2x80x9d, the series of such locations being provided sequentially on the transport mechanism, so that the instrument is always ready to receive each type of object.
According to the invention, the focusing mechanism does not employ translation (Z motion) along the optical axis but rather simulates translation by tilting a plane, on which a flat side of the chip planar holder or the microscope slide is held, about a pre-established hinge axis, or preferably, by tilting about two pre-established, orthogonal axes. It is recognized that tilting a plane about a hinge located at xe2x80x9cinfinityxe2x80x9d can always approximate translation of a small segment of a flat plane in the direction normal to that plane; it is now realized that, within the range of practical microscope instrument geometry and capability, rotating a plane coplanar with a flat object about a defined or pre-established hinge can effectively raise the level of a localized region or point on the plane in a direction essentially normal to its surface, to achieve the desired resolution for a microscope in a practical and low cost manner.
According to a preferred technique of the invention, a plane is fully determined by a line (the defined first hinge) and a point. With the first hinge defined to lie in a plane normal to the optical axis of the microscope, and the flat object being coplanar with it, focusing is achieved by moving xe2x80x9cthe pointxe2x80x9d along a line approximately parallel to the optical axis of the microscope.
In the preferred case, for instance, of scanning a micro lens objective relative to the object to trace a scan line, in which a series of single picture elements (pixels) are registered as the scan line is traced, in the event the top surface of the object inspected along that scan line does not lie in the plane so defined, provision is made according to the invention to rotate the xe2x80x9cfirst hingexe2x80x9d along a pre-established hinge axis orthogonal to both the axis of that xe2x80x9cfirst hingexe2x80x9d and the optical axis of the objective, in order to bring the top surface to be normal to the optical axis. This can be achieved by mounting the first hinge on a support which is coupled to the base of the microscope via a xe2x80x9csecond hingexe2x80x9d that permits a second motion, similar to the first.
Thus, motion for position along the optical axis and motion to maintain orthogonality are accomplished by actively tilting the plane of the object through an arc, or arcs, not by linear translation of the object.
Considerations of the depth of field and the field of view of the objective of a microscope (or the properties of a scanning microscope) guide the selection of the parameters that define such a plane and its two hinges and two movable points.
When a reference flat microscope slide of uniform thickness is located on such a plane, the first hinge and the point can be set such that a region of the top surface of the slide in registry with the optical axis of the microscope is in focus. The second hinge may be omitted especially when the spot size is large and offers sufficient depth of field to avoid frequent correction. If a flat microscope slide of different thickness is later used, adjusting only the movable point can bring the corresponding region of the top surface of that different slide into the focal plane of the objective within practical tolerances. The slide may then be advanced along the plane to bring different regions of the slide into registry with the optical axis.
Relative location of the pre-established hinge and point with respect to the optical axis of the objective is advantageously arranged to simulate the action of a lever, in which the movable point is made to move a relatively large amount compared to the resulting motion of the small segment of the plane that lies at the optical axis. As a result, a comparatively coarse, and therefore low cost, actuator, located at the long end of the lever, can be used to bring the surface of interest into focus by fine movements.
A signal from a sensor can be used to servo the actuator so that the desired region of the top surface of the slide will be in the focal plane of the objective, in line with the optical axis. A number of techniques, e.g. use of a strain gauge at the hinge, or use of optical, capacitive or inductive techniques, can be used to derive a signal to determine the tilted position of the top of the slide.
Also a number of conventional techniques can be used to decide that focus has been reached. The most common techniques analyze the image quality obtained though the microscope objective to drive the actuator until the tilting of the object achieves optimum position of xe2x80x9cbest focusxe2x80x9d.
In the various embodiments, when the microscope slide is mounted on a transport mechanism, the mounting surface of that mechanism is arranged to be parallel to the plane of lateral transport of the microscope slide.
In view of the above, according to one main aspect of the invention, a microscope having an objective with a restricted field of view about an axis for examination or treatment of an approximately flat object along the optical axis is provided, including a tiltable focusing member defining a support plane for the object, the member being mounted to rotate about a pre-established hinge axis to position the object on the member at the focal plane of the microscope, preferably about two hinge axes in the case of scanning in a line, each of which is substantially normal to the optical axis at a distance spaced therefrom, but at angles to each other, preferably orthogonal, and drive mechanisms for rotating the member about both hinge axes are effective to bring into focus the object supported by the member. It should be noted that no translation of the member is necessary for focusing purposes.
Preferred embodiments of this aspect of the invention have one or more of the following features.
The drive mechanism for the first hinge, e.g. the XX hinge, is a driver located outwardly along the tiltable member, more distant from the XX hinge than the position in which the optical axis of the microscope intersects the tiltable member, preferably the distance of the driver from the hinge axis being greater than about twice the distance of the optical axis from the hinge axis.
The drive mechanism for the second hinge, the YY hinge, is suitably located to permit the use of a coarse motion linear motor.
The positions of the drive mechanisms are controlled by an automated control system. In preferred embodiments of this aspect the control system includes a detector that senses the relationship of the object relative to the microscope. In certain preferred cases the detector is a strain gauge or an optical, capacitive or inductive position sensor that senses the height of the object. In a presently particularly preferred case, the detector comprises a light source and a sensor is arranged to determine the height of the object relative to the microscope on the basis of light reflected at an angle from the object. In other preferred cases a through-the-lens image analyzer is constructed and arranged to enable determination of best focus position.
In a preferred embodiment, the first hinge is defined by a reduced thickness of the mounting plate that supports the linear stage holding the object being inspected although in another case a pair of spaced apart flexures that support the tiltable member are employed, preferably the flexures being planar spring members.
The second hinge is similarly preferably defined by a reduced thickness of the mounting plate that supports the first hinge.
A laterally movable carrier is mounted on the tiltable member, the carrier arranged to advance the object, relative to the optical axis. Preferably the direction of advance includes motion in the direction of the radius of the tiltable member. Preferably, a linear guide rail is mounted on the tiltable member, the moveable carrier member movable along the guide, the carrier member having a planar surface for supporting a planar object, the planar surface of the carrier member being parallel to the linear guide. Also, preferably, a driver is arranged to position the carrier member under computer control.
In the form of a scanning microscope, the microscope is constructed and arranged such that the scan axis is normal to both hinge axes, preferably the scanning microscope comprising a moving objective microscope, presently preferred being a microscope in which the moving objective, preferably a micro lens weighing less than 2 grams, is supported upon an oscillating rotary arm that describes an arc generally centered on the axis of the second hinge and on a radial axis of the tiltable member. Preferably the objective has resolution of between about 0.5 and 10 micron and a depth of field of between about 2 and 200 micron.
In the form of a scanning microscope, a controller is provided, constructed to perform dynamic focus by varying the position of the drive mechanism during scanning, preferably the controller responding to through-the-objective image data, and most preferably including a system constructed to determine best focus data for an array of points during a prescan, to store this data, and to employ this data during microscopic examination of the object.
Another aspect of the invention is a microscope for examination of an object along an optical axis, which includes tiltable members defining a support plane for the object, the member being mounted to rotate about a pre-established first hinge axis to position the object on the member at the focal plane of the microscope, the hinge axis lying in a plane substantially normal to the optical axis at a distance spaced therefrom, and a drive mechanism for rotating the member about the hinge axis is effective to bring into focus the object supported by the member, the first hinge axis support being mounted onto a second member which itself is hinged along a second hinge axis substantially normal to both the optical axis and the first hinge axis, the microscope constructed and arranged to scan in a direction transverse to the radial direction of the tiltable member, and a laterally movable carrier is mounted on the tiltable member, the carrier arranged to advance the object, relative to the optical axis, in motion in the direction of the radius of the tiltable member.
In preferred embodiments of this aspect of the invention the scanning microscope comprises a moving objective microscope, preferably in which the microscope includes a flying micro-objective micro lens, and preferably in which the moving objective is supported upon an oscillating rotary arm that describes an arc generally centered on a radial axis of the tiltable member.
Another aspect of the invention is a support member for objects to be inspected by a microscope as described, having a lens member on an oscillating arm, oscillating about axis (Zxe2x80x94Z) in which the hinge axis Xxe2x80x94X is located outwardly beyond the lens-carrying end of the arm, further from the axis ZZ than is the lens.
Preferred embodiments of all of the above aspects and features of the invention are microscopes in which the depth of field is between about 2 and 200 micron, and the drive mechanism is a driver located outwardly along the tiltable member, more distant from the hinge than the position in which the optical axis of the microscope intersects the tiltable member, preferably the distance of the driver from the hinge axis being greater than about twice the distance of the optical axis from the hinge axis.
According to another aspect of the invention a method of microscopic examination is provided comprising providing a microscope for examination of an object along an optical axis, the microscope including tiltable members defining a support plane for the object, the members being mounted to rotate about two defined hinge axes to position the object on the member at the focal plane of the microscope, both hinge axes lying in a plane substantially normal to the optical axis at a distance spaced therefrom, and a respective drive mechanism for rotating each member about its hinge axis, effective to bring into focus the object supported by the member, and under control of an automated control system, moving the movable member to bring the object into the plane of focus of the microscope.
Preferred embodiments of this aspect of the invention have one or more of the following features.
The object comprises biological material.
In certain cases, preferably the object fluoresces and the microscope is constructed to detect such fluorescence, and most preferably the object comprises an ordered array of nucleotides that may fluoresce, preferably the object comprises an ordered array of oligonucleotides or the object comprises an ordered array of deposits of nucleic acid fragments on a biochip or microchip slide.
According to another aspect of the invention, the method of performing quantified fluorescence microscopy comprising providing a microscope according to any of the above designs (such as that shown in FIG. 2A) calibrating the microscope with a calibrating tool having a surface layer of effective fluorophores (such as depicted in FIG. 7 using a calibrating tool such as the calibrating tool of FIG. 9, 10, 11 or 14), and subsequently scanning a slide or biochip having an array or micro array of specimens (as depicted for instance in FIG. 8).
According to another aspect of the invention, any of the microscopes as disclosed, are provided, in a novel way, with a series of dedicated positions, along the Y axis to receive different objects to be scanned, for instance, fluid-spotted microarrays of microscope slides, and biochip reaction modules such as the modules marketed by Affymetrix, Inc., under the brand xe2x80x9cGene Chip(copyright)xe2x80x9d.